That said, these rules are dumb. They work out reasonably well for this particular build at this particular level, but there are a lot of combinations where these rules result in extremely poor bonuses for no good reason. The characters that result are inconsistent with the expectations of the system.

A better method, in general but especially with gestalt, is to incorporate Unearthed Arcana’s “fractional BAB/saves” scheme. In this, you round down after adding up your classes, rather than before. It results in a much cleaner, consistent BAB and saving throw progression.

And then round down for a final saving throw progression of +5/+6/+1. Minor improvement to Reflex, which makes sense because you are taking three different classes with good Reflex saves.

I also strongly recommend eliminating the repeated +2 for each time you take a new class that has a given good save (this is not a part of the Unearthed Arcana variant, however). In this case, you would miss out on the +2 from Swashbuckler 1 and Rogue 1, and have a final, rounded-down saving throw base of +3/+4/+1 – very similar to a typical, single-classed character. This way multiclassing doesn’t have weird positive or negative effects on your saving throws, aside from the natural consequences of having good or bad saving throws.